Starting phenix.real_space_refine on Thu Sep 26 08:57:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vs6_43489/09_2024/8vs6_43489_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vs6_43489/09_2024/8vs6_43489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vs6_43489/09_2024/8vs6_43489.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vs6_43489/09_2024/8vs6_43489.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vs6_43489/09_2024/8vs6_43489_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vs6_43489/09_2024/8vs6_43489_trim.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 5 9.91 5 Mg 1 5.21 5 S 31 5.16 5 C 4055 2.51 5 N 1074 2.21 5 O 1272 1.98 5 H 6015 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12453 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 163 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "A" Number of atoms: 6588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 6588 Classifications: {'peptide': 441} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 419} Chain breaks: 1 Chain: "B" Number of atoms: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 5470 Classifications: {'peptide': 349} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 1, ' MG': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.43, per 1000 atoms: 0.60 Number of scatterers: 12453 At special positions: 0 Unit cell: (72.63, 102.22, 95.495, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 5 19.99 S 31 16.00 Mg 1 11.99 O 1272 8.00 N 1074 7.00 C 4055 6.00 H 6015 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 377 " distance=2.03 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 425 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN C 4 " - " MAN C 5 " ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 6 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1101 " - " ASN A 260 " " NAG B 701 " - " ASN B 360 " " NAG B 702 " - " ASN B 379 " " NAG C 1 " - " ASN A 266 " " NAG D 1 " - " ASN A 44 " " NAG F 1 " - " ASN B 191 " " NAG G 1 " - " ASN B 389 " " NAG H 1 " - " ASN B 414 " Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.0 seconds 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 14 sheets defined 18.6% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'E' and resid 244 through 249 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 122 removed outlier: 4.253A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 128 through 136 Processing helix chain 'B' and resid 161 through 167 removed outlier: 4.622A pdb=" N HIS B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.685A pdb=" N PHE B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.589A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 248 through 256 removed outlier: 3.663A pdb=" N SER B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 3.768A pdb=" N SER B 275 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 305 through 311 removed outlier: 3.526A pdb=" N TYR B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 330 through 344 removed outlier: 3.658A pdb=" N VAL B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.352A pdb=" N ASP A 421 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 411 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A 407 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.911A pdb=" N ASP A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.661A pdb=" N HIS A 113 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.044A pdb=" N LYS A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.678A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.563A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 255 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 283 removed outlier: 3.886A pdb=" N ASP A 325 " --> pdb=" O ARG A 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 348 removed outlier: 6.462A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY A 348 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AB3, first strand: chain 'B' and resid 80 through 85 Processing sheet with id=AB4, first strand: chain 'B' and resid 182 through 189 removed outlier: 6.392A pdb=" N PHE B 146 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N SER B 187 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LEU B 144 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR B 189 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE B 142 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N TYR B 103 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP B 141 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU B 237 " --> pdb=" O PRO B 104 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ASP B 106 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B 239 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR B 108 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N MET B 241 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 110 " --> pdb=" O MET B 241 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL B 297 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N GLY B 322 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N PHE B 299 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 345 through 346 206 hydrogen bonds defined for protein. 525 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.00 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6015 1.03 - 1.23: 14 1.23 - 1.42: 2759 1.42 - 1.62: 3748 1.62 - 1.81: 48 Bond restraints: 12584 Sorted by residual: bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.578 -0.059 2.00e-02 2.50e+03 8.78e+00 bond pdb=" N GLY E 240 " pdb=" CA GLY E 240 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.04e+00 bond pdb=" C3 BMA C 3 " pdb=" O3 BMA C 3 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.04e+00 bond pdb=" C1 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sigma weight residual 1.410 1.446 -0.036 2.00e-02 2.50e+03 3.32e+00 bond pdb=" C2 MAN C 4 " pdb=" O2 MAN C 4 " ideal model delta sigma weight residual 1.407 1.442 -0.035 2.00e-02 2.50e+03 3.01e+00 ... (remaining 12579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 22011 1.70 - 3.40: 498 3.40 - 5.10: 65 5.10 - 6.80: 7 6.80 - 8.49: 2 Bond angle restraints: 22583 Sorted by residual: angle pdb=" CB GLN B 353 " pdb=" CG GLN B 353 " pdb=" CD GLN B 353 " ideal model delta sigma weight residual 112.60 117.65 -5.05 1.70e+00 3.46e-01 8.81e+00 angle pdb=" C1 BMA C 3 " pdb=" O5 BMA C 3 " pdb=" C5 BMA C 3 " ideal model delta sigma weight residual 118.82 110.33 8.49 3.00e+00 1.11e-01 8.02e+00 angle pdb=" N VAL A 312 " pdb=" CA VAL A 312 " pdb=" C VAL A 312 " ideal model delta sigma weight residual 113.42 110.29 3.13 1.17e+00 7.31e-01 7.18e+00 angle pdb=" N ASP A 148 " pdb=" CA ASP A 148 " pdb=" C ASP A 148 " ideal model delta sigma weight residual 107.73 104.23 3.50 1.34e+00 5.57e-01 6.82e+00 angle pdb=" C3 MAN C 4 " pdb=" C2 MAN C 4 " pdb=" O2 MAN C 4 " ideal model delta sigma weight residual 111.77 104.42 7.35 3.00e+00 1.11e-01 6.01e+00 ... (remaining 22578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.85: 5608 20.85 - 41.71: 426 41.71 - 62.56: 148 62.56 - 83.42: 26 83.42 - 104.27: 12 Dihedral angle restraints: 6220 sinusoidal: 3507 harmonic: 2713 Sorted by residual: dihedral pdb=" CA ASP A 353 " pdb=" C ASP A 353 " pdb=" N GLY A 354 " pdb=" CA GLY A 354 " ideal model delta harmonic sigma weight residual -180.00 -160.37 -19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA SER A 29 " pdb=" C SER A 29 " pdb=" N ALA A 30 " pdb=" CA ALA A 30 " ideal model delta harmonic sigma weight residual 180.00 160.57 19.43 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual 93.00 60.65 32.35 1 1.00e+01 1.00e-02 1.49e+01 ... (remaining 6217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 797 0.052 - 0.103: 145 0.103 - 0.154: 62 0.154 - 0.206: 2 0.206 - 0.257: 2 Chirality restraints: 1008 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C2 BMA C 3 " pdb=" C1 BMA C 3 " pdb=" C3 BMA C 3 " pdb=" O2 BMA C 3 " both_signs ideal model delta sigma weight residual False 2.47 2.70 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.38 0.02 2.00e-02 2.50e+03 1.10e+00 ... (remaining 1005 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 353 " 0.009 2.00e-02 2.50e+03 1.96e-02 5.79e+00 pdb=" CD GLN B 353 " -0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN B 353 " 0.020 2.00e-02 2.50e+03 pdb=" NE2 GLN B 353 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 353 " 0.010 2.00e-02 2.50e+03 pdb="HE22 GLN B 353 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 365 " -0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO B 366 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 366 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 366 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 419 " 0.012 2.00e-02 2.50e+03 9.08e-03 2.47e+00 pdb=" CG TYR A 419 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 419 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 419 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 419 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 419 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 419 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 419 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TYR A 419 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR A 419 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR A 419 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR A 419 " -0.000 2.00e-02 2.50e+03 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1016 2.22 - 2.81: 25880 2.81 - 3.41: 33810 3.41 - 4.00: 48350 4.00 - 4.60: 72235 Nonbonded interactions: 181291 Sorted by model distance: nonbonded pdb=" O ASN A 2 " pdb=" H ARG A 438 " model vdw 1.622 2.450 nonbonded pdb=" O PHE B 299 " pdb=" H GLY B 322 " model vdw 1.631 2.450 nonbonded pdb="HH11 ARG A 115 " pdb=" O THR A 116 " model vdw 1.647 2.450 nonbonded pdb=" H ASP A 257 " pdb=" O SER A 262 " model vdw 1.659 2.450 nonbonded pdb=" HZ3 LYS A 104 " pdb=" OD1 ASP A 167 " model vdw 1.679 2.450 ... (remaining 181286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 31.800 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6569 Z= 0.283 Angle : 0.737 8.494 8892 Z= 0.377 Chirality : 0.049 0.257 1008 Planarity : 0.004 0.060 1148 Dihedral : 16.491 104.269 2662 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.65 % Allowed : 16.34 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.29), residues: 791 helix: -0.58 (0.51), residues: 99 sheet: 0.49 (0.31), residues: 266 loop : -0.51 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 230 HIS 0.003 0.001 HIS B 98 PHE 0.009 0.001 PHE A 88 TYR 0.025 0.002 TYR A 419 ARG 0.004 0.001 ARG B 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 TYR cc_start: 0.8415 (m-80) cc_final: 0.7898 (m-80) outliers start: 11 outliers final: 12 residues processed: 85 average time/residue: 2.3697 time to fit residues: 212.6182 Evaluate side-chains 78 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 357 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 352 GLN B 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6569 Z= 0.349 Angle : 0.652 5.182 8892 Z= 0.345 Chirality : 0.050 0.248 1008 Planarity : 0.005 0.055 1148 Dihedral : 9.577 81.142 1228 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.70 % Allowed : 15.89 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.29), residues: 791 helix: -0.93 (0.49), residues: 106 sheet: 0.17 (0.30), residues: 264 loop : -0.57 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 230 HIS 0.004 0.001 HIS B 227 PHE 0.015 0.002 PHE A 217 TYR 0.026 0.002 TYR A 275 ARG 0.004 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8669 (OUTLIER) cc_final: 0.8403 (p-90) REVERT: A 275 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7422 (m-10) REVERT: A 316 SER cc_start: 0.8035 (OUTLIER) cc_final: 0.7827 (p) REVERT: A 369 LYS cc_start: 0.7119 (mtmm) cc_final: 0.6836 (mtpp) REVERT: B 80 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7153 (tp30) outliers start: 18 outliers final: 10 residues processed: 85 average time/residue: 2.1743 time to fit residues: 196.4071 Evaluate side-chains 84 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 416 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 320 GLN B 161 HIS B 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6569 Z= 0.341 Angle : 0.641 5.513 8892 Z= 0.336 Chirality : 0.049 0.218 1008 Planarity : 0.005 0.044 1148 Dihedral : 8.778 65.029 1220 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.65 % Allowed : 15.44 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.28), residues: 791 helix: -1.02 (0.48), residues: 106 sheet: -0.11 (0.30), residues: 264 loop : -0.66 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 230 HIS 0.004 0.001 HIS B 180 PHE 0.016 0.002 PHE A 19 TYR 0.027 0.002 TYR A 275 ARG 0.004 0.001 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 74 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8700 (OUTLIER) cc_final: 0.8311 (p-90) REVERT: A 275 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.7480 (m-10) REVERT: A 329 THR cc_start: 0.8467 (m) cc_final: 0.8134 (t) REVERT: A 353 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7291 (m-30) REVERT: A 369 LYS cc_start: 0.6956 (mtmm) cc_final: 0.6721 (mtpp) REVERT: A 390 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8458 (mp) REVERT: B 80 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7240 (tp30) outliers start: 31 outliers final: 16 residues processed: 96 average time/residue: 2.1160 time to fit residues: 217.6795 Evaluate side-chains 94 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 73 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 416 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 chunk 43 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN B 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6569 Z= 0.265 Angle : 0.597 5.426 8892 Z= 0.310 Chirality : 0.048 0.241 1008 Planarity : 0.004 0.039 1148 Dihedral : 8.153 56.039 1220 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.30 % Allowed : 17.09 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.28), residues: 791 helix: -0.82 (0.50), residues: 106 sheet: -0.19 (0.30), residues: 263 loop : -0.70 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 230 HIS 0.004 0.001 HIS A 113 PHE 0.012 0.002 PHE A 19 TYR 0.025 0.002 TYR A 275 ARG 0.003 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8688 (OUTLIER) cc_final: 0.8281 (p-90) REVERT: A 115 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7529 (ptm160) REVERT: A 329 THR cc_start: 0.8523 (m) cc_final: 0.8171 (t) REVERT: A 369 LYS cc_start: 0.6992 (mtmm) cc_final: 0.6757 (mtpp) REVERT: A 430 ASP cc_start: 0.7769 (m-30) cc_final: 0.7528 (m-30) REVERT: B 80 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7150 (tp30) REVERT: B 202 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.6592 (tm-30) outliers start: 22 outliers final: 14 residues processed: 92 average time/residue: 2.2490 time to fit residues: 219.2357 Evaluate side-chains 93 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 416 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN B 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6569 Z= 0.240 Angle : 0.582 5.553 8892 Z= 0.301 Chirality : 0.047 0.231 1008 Planarity : 0.004 0.038 1148 Dihedral : 7.682 49.147 1220 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.60 % Allowed : 17.39 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.29), residues: 791 helix: -0.67 (0.51), residues: 106 sheet: -0.28 (0.30), residues: 263 loop : -0.68 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 230 HIS 0.003 0.001 HIS B 118 PHE 0.011 0.002 PHE A 19 TYR 0.024 0.002 TYR A 275 ARG 0.003 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 75 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8677 (OUTLIER) cc_final: 0.8234 (p-90) REVERT: A 115 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7566 (ptm160) REVERT: A 329 THR cc_start: 0.8611 (m) cc_final: 0.8275 (t) REVERT: A 353 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7190 (m-30) REVERT: A 369 LYS cc_start: 0.7018 (mtmm) cc_final: 0.6781 (mtpp) REVERT: A 390 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8427 (mp) REVERT: A 430 ASP cc_start: 0.7761 (m-30) cc_final: 0.7546 (m-30) REVERT: B 84 GLN cc_start: 0.6596 (pm20) cc_final: 0.6352 (pm20) REVERT: B 202 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7969 (mm-40) REVERT: B 278 MET cc_start: 0.8390 (ptp) cc_final: 0.7781 (ptp) REVERT: B 302 GLN cc_start: 0.8155 (tt0) cc_final: 0.7910 (tt0) outliers start: 24 outliers final: 15 residues processed: 92 average time/residue: 2.2699 time to fit residues: 221.1329 Evaluate side-chains 92 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 416 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 55 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN B 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6569 Z= 0.206 Angle : 0.562 5.621 8892 Z= 0.290 Chirality : 0.047 0.220 1008 Planarity : 0.004 0.035 1148 Dihedral : 7.227 54.473 1220 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.85 % Allowed : 17.99 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.29), residues: 791 helix: -0.55 (0.51), residues: 106 sheet: -0.29 (0.30), residues: 263 loop : -0.66 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 230 HIS 0.002 0.001 HIS A 113 PHE 0.009 0.001 PHE A 88 TYR 0.022 0.001 TYR A 275 ARG 0.002 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8650 (OUTLIER) cc_final: 0.8240 (p-90) REVERT: A 115 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7554 (ptm160) REVERT: A 329 THR cc_start: 0.8606 (m) cc_final: 0.8290 (t) REVERT: A 353 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7298 (m-30) REVERT: A 369 LYS cc_start: 0.7026 (mtmm) cc_final: 0.6793 (mtpp) REVERT: A 430 ASP cc_start: 0.7762 (m-30) cc_final: 0.7556 (m-30) REVERT: B 80 GLU cc_start: 0.7547 (tt0) cc_final: 0.7258 (tt0) REVERT: B 84 GLN cc_start: 0.6571 (pm20) cc_final: 0.6193 (pm20) REVERT: B 202 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7841 (mm-40) REVERT: B 278 MET cc_start: 0.8421 (ptp) cc_final: 0.7817 (ptp) REVERT: B 302 GLN cc_start: 0.8034 (tt0) cc_final: 0.7785 (tt0) outliers start: 19 outliers final: 11 residues processed: 89 average time/residue: 2.2773 time to fit residues: 214.4101 Evaluate side-chains 89 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 416 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 152 GLN B 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6569 Z= 0.288 Angle : 0.595 5.750 8892 Z= 0.307 Chirality : 0.048 0.223 1008 Planarity : 0.004 0.037 1148 Dihedral : 7.209 59.531 1217 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.90 % Allowed : 17.24 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.29), residues: 791 helix: -0.60 (0.51), residues: 106 sheet: -0.36 (0.31), residues: 264 loop : -0.67 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 230 HIS 0.003 0.001 HIS B 307 PHE 0.012 0.002 PHE A 19 TYR 0.024 0.002 TYR A 275 ARG 0.003 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 74 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8685 (OUTLIER) cc_final: 0.8334 (p-90) REVERT: A 115 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7593 (ptm160) REVERT: A 329 THR cc_start: 0.8572 (m) cc_final: 0.8272 (t) REVERT: A 353 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7386 (m-30) REVERT: A 369 LYS cc_start: 0.7145 (mtmm) cc_final: 0.6870 (mtpp) REVERT: A 390 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8441 (mp) REVERT: A 430 ASP cc_start: 0.7828 (m-30) cc_final: 0.7593 (m-30) REVERT: B 80 GLU cc_start: 0.7646 (tt0) cc_final: 0.7423 (tt0) REVERT: B 84 GLN cc_start: 0.6601 (pm20) cc_final: 0.6179 (pm20) REVERT: B 202 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.6307 (tm-30) REVERT: B 278 MET cc_start: 0.8421 (ptp) cc_final: 0.7814 (ptp) REVERT: B 302 GLN cc_start: 0.8094 (tt0) cc_final: 0.7844 (tt0) outliers start: 26 outliers final: 17 residues processed: 93 average time/residue: 2.2357 time to fit residues: 220.3396 Evaluate side-chains 95 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 73 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 416 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 69 optimal weight: 0.0470 chunk 72 optimal weight: 0.8980 chunk 66 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN B 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6569 Z= 0.185 Angle : 0.549 5.484 8892 Z= 0.283 Chirality : 0.046 0.206 1008 Planarity : 0.004 0.032 1148 Dihedral : 6.422 42.736 1213 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.30 % Allowed : 17.84 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.29), residues: 791 helix: -0.38 (0.52), residues: 106 sheet: -0.32 (0.30), residues: 263 loop : -0.60 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 230 HIS 0.002 0.001 HIS B 118 PHE 0.009 0.001 PHE A 88 TYR 0.021 0.001 TYR A 275 ARG 0.002 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8660 (OUTLIER) cc_final: 0.8299 (p-90) REVERT: A 329 THR cc_start: 0.8612 (m) cc_final: 0.8286 (t) REVERT: A 353 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6592 (m-30) REVERT: A 369 LYS cc_start: 0.7126 (mtmm) cc_final: 0.6857 (mtpp) REVERT: A 390 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8425 (mp) REVERT: A 430 ASP cc_start: 0.7810 (m-30) cc_final: 0.7585 (m-30) REVERT: B 80 GLU cc_start: 0.7655 (tt0) cc_final: 0.7425 (tt0) REVERT: B 84 GLN cc_start: 0.6504 (pm20) cc_final: 0.6160 (pm20) REVERT: B 202 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7814 (mm-40) REVERT: B 278 MET cc_start: 0.8409 (ptp) cc_final: 0.7798 (ptp) REVERT: B 302 GLN cc_start: 0.8027 (tt0) cc_final: 0.7774 (tt0) outliers start: 22 outliers final: 12 residues processed: 94 average time/residue: 2.2447 time to fit residues: 223.6966 Evaluate side-chains 90 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 362 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 46 optimal weight: 0.3980 chunk 75 optimal weight: 0.7980 chunk 45 optimal weight: 0.0980 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 384 ASN B 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6569 Z= 0.191 Angle : 0.546 5.642 8892 Z= 0.279 Chirality : 0.046 0.190 1008 Planarity : 0.004 0.047 1148 Dihedral : 6.104 42.954 1213 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.15 % Allowed : 18.14 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.29), residues: 791 helix: -0.27 (0.52), residues: 106 sheet: -0.34 (0.31), residues: 263 loop : -0.58 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 230 HIS 0.002 0.001 HIS B 98 PHE 0.009 0.001 PHE A 88 TYR 0.020 0.001 TYR A 275 ARG 0.006 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8680 (OUTLIER) cc_final: 0.8254 (p-90) REVERT: A 115 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7678 (ptm160) REVERT: A 329 THR cc_start: 0.8617 (m) cc_final: 0.8301 (t) REVERT: A 353 ASP cc_start: 0.6974 (OUTLIER) cc_final: 0.6660 (m-30) REVERT: A 369 LYS cc_start: 0.7144 (mtmm) cc_final: 0.6873 (mtpp) REVERT: A 390 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8412 (mp) REVERT: B 80 GLU cc_start: 0.7690 (tt0) cc_final: 0.7440 (tt0) REVERT: B 84 GLN cc_start: 0.6511 (pm20) cc_final: 0.6174 (pm20) REVERT: B 202 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7802 (mm-40) REVERT: B 278 MET cc_start: 0.8343 (ptp) cc_final: 0.7729 (ptp) REVERT: B 302 GLN cc_start: 0.8033 (tt0) cc_final: 0.7781 (tt0) outliers start: 21 outliers final: 13 residues processed: 91 average time/residue: 2.1991 time to fit residues: 212.7214 Evaluate side-chains 91 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 362 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.3980 chunk 72 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN B 125 ASN B 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6569 Z= 0.226 Angle : 0.560 5.584 8892 Z= 0.287 Chirality : 0.047 0.188 1008 Planarity : 0.004 0.040 1148 Dihedral : 6.135 43.466 1213 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.00 % Allowed : 18.44 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.29), residues: 791 helix: -0.30 (0.52), residues: 106 sheet: -0.38 (0.31), residues: 264 loop : -0.56 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 230 HIS 0.003 0.001 HIS A 113 PHE 0.010 0.002 PHE A 19 TYR 0.020 0.002 TYR A 275 ARG 0.002 0.000 ARG B 236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 70 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.8699 (OUTLIER) cc_final: 0.8267 (p-90) REVERT: A 115 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7615 (ptm160) REVERT: A 164 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7543 (m) REVERT: A 329 THR cc_start: 0.8682 (m) cc_final: 0.8386 (t) REVERT: A 369 LYS cc_start: 0.7206 (mtmm) cc_final: 0.6925 (mtpp) REVERT: A 390 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8439 (mp) REVERT: B 84 GLN cc_start: 0.6519 (pm20) cc_final: 0.6187 (pm20) REVERT: B 202 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7812 (mm-40) REVERT: B 278 MET cc_start: 0.8339 (ptp) cc_final: 0.7721 (ptp) REVERT: B 302 GLN cc_start: 0.8053 (tt0) cc_final: 0.7804 (tt0) outliers start: 20 outliers final: 12 residues processed: 88 average time/residue: 2.3480 time to fit residues: 219.1671 Evaluate side-chains 86 residues out of total 667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 69 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 362 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 chunk 3 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN B 125 ASN B 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.163816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.142216 restraints weight = 19283.085| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.59 r_work: 0.3609 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6569 Z= 0.212 Angle : 0.557 5.698 8892 Z= 0.286 Chirality : 0.046 0.181 1008 Planarity : 0.004 0.044 1148 Dihedral : 6.053 43.349 1213 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.85 % Allowed : 18.74 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.29), residues: 791 helix: -0.23 (0.52), residues: 106 sheet: -0.38 (0.31), residues: 264 loop : -0.55 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 230 HIS 0.002 0.001 HIS B 307 PHE 0.010 0.002 PHE A 19 TYR 0.019 0.001 TYR A 275 ARG 0.003 0.000 ARG A 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5572.23 seconds wall clock time: 96 minutes 44.41 seconds (5804.41 seconds total)